Blender Reads Some Videos' Frames Incorrectly (duplicates + skipping)
Blender is very picky about source codecs. Try creating a proxy with timecode (bottom VSE Clip menu). 
You could also try turning on MPEG preseek in the Strip Properties menu by entering a frame value higher than 0. This enables Blender to cache a portion of the source making it easier to decode. It may slow performance of playback

If that doesn't work try converting the media to a codec that Blender prefers. Make sure that the codec that you use has a fixed frame rate. Variable frame rate screen captures will fail.